A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta)
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and m...
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ftpubmed:oai:pubmedcentral.nih.gov:10320755 2023-07-30T04:04:25+02:00 A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) Squires, Theodore E Rödin-Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C Melsted, Páll Höglund, Jacob Magnússon, Kristinn Pétur 2023-05-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320755/ http://www.ncbi.nlm.nih.gov/pubmed/37141262 https://doi.org/10.1093/g3journal/jkad099 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320755/ http://www.ncbi.nlm.nih.gov/pubmed/37141262 http://dx.doi.org/10.1093/g3journal/jkad099 © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. G3 (Bethesda) Genome Report Text 2023 ftpubmed https://doi.org/10.1093/g3journal/jkad099 2023-07-09T01:07:45Z The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes). Text Iceland Lagopus muta rock ptarmigan PubMed Central (PMC) G3: Genes, Genomes, Genetics 13 7 |
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topic |
Genome Report |
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Genome Report Squires, Theodore E Rödin-Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C Melsted, Páll Höglund, Jacob Magnússon, Kristinn Pétur A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
topic_facet |
Genome Report |
description |
The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes). |
format |
Text |
author |
Squires, Theodore E Rödin-Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C Melsted, Páll Höglund, Jacob Magnússon, Kristinn Pétur |
author_facet |
Squires, Theodore E Rödin-Mörch, Patrik Formenti, Giulio Tracey, Alan Abueg, Linelle Brajuka, Nadolina Jarvis, Erich Halapi, Eva C Melsted, Páll Höglund, Jacob Magnússon, Kristinn Pétur |
author_sort |
Squires, Theodore E |
title |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_short |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_full |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_fullStr |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_full_unstemmed |
A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta) |
title_sort |
chromosome-level genome assembly for the rock ptarmigan (lagopus muta) |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320755/ http://www.ncbi.nlm.nih.gov/pubmed/37141262 https://doi.org/10.1093/g3journal/jkad099 |
genre |
Iceland Lagopus muta rock ptarmigan |
genre_facet |
Iceland Lagopus muta rock ptarmigan |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320755/ http://www.ncbi.nlm.nih.gov/pubmed/37141262 http://dx.doi.org/10.1093/g3journal/jkad099 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/g3journal/jkad099 |
container_title |
G3: Genes, Genomes, Genetics |
container_volume |
13 |
container_issue |
7 |
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1772815844453122048 |